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Acta Agronomica Sinica ›› 2018, Vol. 44 ›› Issue (9): 1263-1273.doi: 10.3724/SP.J.1006.2018.01263

• RESEARCH PAPERS •     Next Articles

Genotyping of SCN, SMV Resistance, Salinity Tolerance and Screening of Pyramiding Favorable Alleles in Introduced Soybean Accessions

Jun-Hua YE1,2(),Qi-Tai YANG2,3,Zhang-Xiong LIU2,Yong GUO2,Ying-Hui LI2,Rong-Xia GUAN2,Li-Juan QIU2,*   

  1. 1 College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
    2 National Key Facility for Gene Resources and Genetic Improvement / Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    3 Department of Biotechnology, Bengbu Medical College, Bengbu 233000, Anhui, China
  • Received:2018-03-04 Accepted:2018-06-12 Online:2018-09-10 Published:2018-07-02
  • Contact: Li-Juan QIU E-mail:yejunhua1994@qq.com
  • Supported by:
    This study was supported by the National Key R&D Program(2016 YFD0100304);This study was supported by the National Key R&D Program(2016YFD0100304);the Agricultural Science and Technology Innovation Program of CAAS


China has introduced 3218 soybean accessions from 26 countries such as the United States, Russia and Japan, and some of them have been carried out soybean cyst nematode (SCN), soybean mosaic virus (SMV) and salinity tolerance resistance evaluation. However, the systematic genotyping of these accessions has not been reported yet. In this study, five robust functional markers have been developed for KASP assays, three SCN loci (rhg1, Rhg4, SCN3-11) and salinity tolerance gene (GmSALT3) included. A total of 1489 introduced soybean accessions were genotyped by these markers with high-throughput assay as well as a SCAR marker (SCN11) which is related to soybean mosaic virus resistance. The results showed that there were 1084 accessions detected with favorable alleles; where accessions detected with resistant alleles at three loci were as much as 19, including three pyramiding SCN genes (rhg1, Rhg4, SCN3-11) which were Peking type and seven pyramiding SCN and SMV , two pyramiding SCN and salinity favorable alleles, as well as seven pyramiding SCN, SMV and salinity favorable alleles; and accessions detected with four favorable alleles were as much as nine accessions, including six pyramiding SCN and SMV resistance alleles, one accession detected with SCN and salinity tolerance and two detected with SCN, SMV and salinity favorable alleles, eight detected with all the favorable alleles in this study. Among the elite accessions mentioned above, it has been proved that 44 accessions resistant to SCN, SMV-3 or tolerant to salinity. Among the 36 accessions with three or more favorable alleles, 52.78% had been reported of one or two characteristics. Among the accessions without resistance or tolerance alleles, it has been reported that 93 accessions were tolerant to salinity or resistant to SMV-3, where new resistance or tolerance genes could be found. Screening out the accessions with high-throughput SNP detection assays for resistance and tolerance alleles in soybean provides information for their further phenotyping, screening and breeding.

Key words: soybean germplasm, molecular markers, KASP, genotyping

Table 1

Types of SCN resistance, SMV resistance, and salinity tolerance markers and primer sequences"

Primer sequence (5°-3°)
大豆胞囊线虫抗性 SCN resistance
Rhg4-389 KASP Glyma08g11490 Rhg4-COM: CTACACCGCCGTCCTCAAC [17]
大豆耐盐性 Soybean salinity tolerance
大豆花叶病毒抗性 SMV resistance

Fig. 1

Partial germplasms genotyping results with KASP and SCAR markerA-E: each dot corresponds to an accession tested. Red or blue dots represent homozygous genotypes; green dots represent heterozygotes; pink dots represent no signal detected or weak signals; purple dots represent signals which cannot be classified; black dots represent NTC, no template control. F: M is DL2000; 1, 3 represent sensitivity to soybean mosaic virus; 2, 4 represent resistance to soybean mosaic virus."

Table 2

Genotyping results with six resistance/tolerance markers for introduced accessions"

effectively identified No.
Corresponding phenotype 1)
Size (No.)
Ratio (%)
SCN resistance
rhg1 1383 G/G R 31 2.24
C/C S 1352 97.76
Rhg4-389 1480 G/G R 37 2.50
C/C S 1441 97.37
SCN3-11 1356 T/T R 66 4.87
C/C S 1290 95.13
Soybean salinity tolerance
SALT3 1380 -/- 236 17.10
T/T S 1127 81.67
Ncl-5 1479 G/G 1384 93.58
A/A S 85 5.75
SALT3, Ncl-5 1380 SALT3(H1) T 235 17.03
SMV resistance
SCN11 1489 R 960 64.47
S 529 35.53

Fig. 2

Distribution and origins of resistant alleles or haplotype in five loci"

Table 3

Screening the introduced germplasms using five loci"

Favorable allele
携带优异等位基因的种质 Germplasm with favorable alleles
Size (No.)
Ratio (%)
Representative germplasm
单位点 Single locus 901 60.51
SCN SCN3-11 15 1.01 中特1号 Zhongte 1
SMV SCN11 796 53.46 Provar
Salt SALT3(H1) 90 6.04 Harosoy 71
双位点 Two loci 147 9.87
SCN rhg1/Rhg4 1 0.07 M044
SCN Rhg4/SCN3-11 2 0.13 PR 149-3
SCN, SMV rhg1/SCN11 2 0.13 PI576145
SCN, SMV Rhg4/SCN11 5 0.34 Mack
SCN, SMV SCN3-11/SCN11 12 0.81 CA50
SCN, Salt SCN3-11/SALT3(H1) 8 0.54 PI590579
SCN, Salt Rhg4/SALT3(H1) 2 0.13 D85-10412
SMV, Salt SALT3(H1)/SCN11 115 7.72 Lee 68
3个位点 Three loci 19 1.28
SCN rhg1/Rhg4/SCN3-11 3 0.20 Centennial
SCN, SMV rhg1/Rhg4/SCN11 2 0.13 Delsoy4900
SCN, SMV rhg1/SCN3-11/SCN11 4 0.27 AGS175
SCN, SMV Rhg4/SCN3-11/SCN11 1 0.07 9234
SCN, Salt rhg1/Rhg4/SALT3(H1) 1 0.07 T221
SCN, Salt Rhg4/SCN3-11/SALT3(H1) 1 0.07 LINE272H选 LINE272H Xuan
SCN, SMV, Salt rhg1/SALT3(H1)/SCN11 2 0.13 H6255RR
SCN, SMV, Salt Rhg4/SALT3(H1)/SCN11 2 0.13 Lamar
SCN, SMV, Salt SCN3-11/SALT3(H1)/SCN11 3 0.20 P951341RR
4个位点 Four loci 9 0.60
SCN, SMV rhg1/Rhg4/SCN3-11/SCN11 6 0.40 Newton
SCN, Salt rhg1/Rhg4/SCN3-11/SALT3(H1) 1 0.07 PI90763
SCN, SMV, Salt rhg1/SCN3-11/SALT3(H1)/SCN11 1 0.07 S01-9364
SCN, SMV, Salt Rhg4/SCN3-11/SALT3(H1)/SCN11 1 0.07 S-10-1
5个位点 Five loci 8 0.54
SCN, SMV, Salt rhg1/Rhg4/SCN3-11/SALT3(H1)/SCN11 8 0.54 Pin-din-guan


Number of resistant loci
Accession No.
Favorable alleles
3个位点 Three loci WDD00828 Centennial rhg1, Rhg4, SCN3-11 SCN*
WDD01994 M87-1569 rhg1, Rhg4, SCN3-11 SCN*
WDD00691 AGS272+ rhg1, Rhg4, SCN3-11 SCN*
WDD03200 LINE272H Xuan# Rhg4, SCN3-11, SALT3(H1) SCN, Salt
WDD00289 T221 rhg1, Rhg4, SALT3(H1) SCN*, Salt
WDD00858 N80-2317# rhg1, SCN3-11, SCN11 SCN, SMV
WDD00859 N80-50232# rhg1, SCN3-11, SCN11 SCN, SMV
WDD00666 AGS65+ rhg1, SCN3-11, SCN11 SCN, SMV
Number of resistant loci
Accession No.
Favorable alleles
WDD00683 AGS175+ rhg1, SCN3-11, SCN11 SCN, SMV
WDD02019 9234 Rhg4, SCN3-11, SCN11 SCN*, SMV
WDD01607 Delsoy4900 rhg1, Rhg4, SCN11 SCN*, SMV
WDD03086 G04-Ben229lR-M rhg1, Rhg4, SCN11 SCN, SMV
WDD02211 H6255 rhg1, SALT3(H1), SCN11 SCN, Salt, SMV
WDD03205 M017-1# rhg1, SALT3(H1), SCN11 SCN, Salt, SMV
WDD00916 SRE-D-14A# Rhg4, SALT3(H1), SCN11 SCN, Salt, SMV
WDD01640 Lamar Rhg4, SALT3(H1), SCN11 SCN*, Salt, SMV
WDD00334 Clark-G SCN3-11, SALT3(H1), SCN11 SCN, Salt, SMV
WDD02252 P951341 SCN3-11, SALT3(H1), SCN11 SCN, Salt, SMV
WDD00335 Clark-S SCN3-11, SALT3(H1), SCN11 SCN, Salt, SMV
4个位点 Four loci WDD02102 PI90763 rhg1, Rhg4, SCN3-11, Salt3(H1) SCN*, Salt
WDD00926 TGX814-26D# rhg1, Rhg4, SCN3-11, SCN11 SCN, SMV
WDD01583 Newton rhg1, Rhg4, SCN3-11, SCN11 SCN*, SMV
WDD00595 Custer rhg1, Rhg4, SCN3-11, SCN11 SCN*, SMV
WDD00602 Franklin rhg1, Rhg4, SCN3-11, SCN11 SCN*, SMV
WDD02015 TBD rhg1, Rhg4, SCN3-11, SCN11 SCN, SMV
WDD01538 rhg1, Rhg4, SCN3-11, SCN11 SCN, SMV
WDD03083 S01-9364 rhg1, SCN3-11, SALT3(H1), SCN11 SCN*, Salt*, SMV
WDD00774 S-10-1 Rhg4, SCN3-11, SALT3(H1), SCN11 SCN, Salt, SMV
5个位点 Five loci WDD03084 S01-9391 rhg1, Rhg4, SCN3-11, SALT3(H1), SCN11 SCN*, Salt, SMV
WDD01632 Bryan rhg1, Rhg4, SCN3-11, SALT3(H1), SCN11 SCN*, Salt, SMV
WDD01614 Rhodes rhg1, Rhg4, SCN3-11, SALT3(H1), SCN11 SCN*, Salt, SMV
WDD00721 Forrest rhg1, Rhg4, SCN3-11, SALT3(H1), SCN11 SCN*, Salt, SMV
WDD01971 D83-3349 rhg1, Rhg4, SCN3-11, SALT3(H1), SCN11 SCN*, Salt, SMV
WDD00661 A-66 Jia+ rhg1, Rhg4, SCN3-11, SALT3(H1), SCN11 SCN, Salt, SMV
WDD02989 Pin-din-guan rhg1, Rhg4, SCN3-11, SALT3(H1), SCN11 SCN*, Salt*, SMV
WDD03094 S99-2281 rhg1, Rhg4, SCN3-11, SALT3(H1), SCN11 SCN*, Salt, SMV
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